I'd like to confirm this. When typing in Skype and playing FTL (non-steam version), I find that suddenly my keystrokes aren't being accepted by the program, and instead going into the chat window,.Happens when I'm having a Steam chat with someone, I alt-tab to another porgram, and then they post something to the chat window when I'm on the other program. Suddenly, none of my keyboard commands to the space ship in FTL work, and when I switch to the Steam chat window, all my keystrokes are there.

This isn't just limited to actual chat messages, btw; I found that whenever my friends joined a game, whatever I was looking at would lose focus and the "Friend is playing <X>" notification would gain it. The application would regain focus when the notification went away.